life the science of biology 7th ed - bill purves, david sadava

Monster frogs—what a great topic for an undergraduate research
project! That’s what Stanford University sophomore Pieter John-
son thought when he was shown a jar of Pacific tree frogs with ex-
tra legs growing out of their bodies. The frogs were collected from
a pond on a farm close to the old Almaden mercury mines south
of San Jose, California. Scientists from all over the world were reporting alarming de-
clines in populations of many different kinds of frogs, so perhaps these “monster”
frogs would hold a clue to why frogs all over the world are in trouble. Possible causes
of the deformities could have been agricultural chemicals or heavy metals leaching
out of the old mines. Library research, however, suggested other possibilities to Pieter.
Pieter studied 35 ponds in the region where the deformed frogs had been found.
He counted frogs in the ponds and measured chemicals in the water. Thirteen of the
ponds had Pacific tree frogs, but deformed frogs were found in only four ponds. To
Pieter’s surprise, analysis of the water samples failed to reveal higher amounts of
pesticides, industrial chemicals, or heavy metals in the ponds with deformed frogs.
Also surprisingly, when he collected eggs from those ponds and hatched them in the
laboratory, he always got normal frogs. The only difference he observed among the
ponds he studied was that the ponds with the deformed frogs also contained fresh-
water snails.
Freshwater snails are hosts for many
parasites. Many parasites go through
complex life cycles with several stages,
each of which requires a specific host
animal. Pieter focused on the possibil-
ity that some parasite that used fresh-
water snails as intermediate hosts was
infecting the frogs and causing their de-
formities. Pieter found a candidate with
this type of life cycle: a small flatworm
called Ribeiroia, which was present in
the ponds where the deformed frogs

were found.
Pieter then did an experiment. He
collected frog eggs from regions where
there were no records of deformed
frogs or of Ribeiroia. He hatched the
eggs in the laboratory in containers
with and without the parasite. When
the parasite was present in the contain-
An Evolutionary Framework for Biology
A Monster Phenomenon As a college
sophomore,Pieter Johnson studied ponds
that were home to Pacific tree frogs (Hyla
regilla), trying to discover a reason for the
presence of so many deformed frogs.
What appears in the inset to be a tail is
an extra leg.
1
ers, 85 percent of the frogs developed deformities. Further
experiments showed why not all the frogs were deformed:
The infection had to occur before a tadpole started to grow
legs. When tadpoles with already developing legs were in-
fected, they did not become deformed.
Pieter’s project started with a question based on an ob-
servation in nature. He formulated several possible answers,
made observations to narrow down the list of answers, and
then did experiments to test what he thought was the most
likely answer. His experiments enabled him to reach a con-
clusion: that these deformities were caused by Ribeiroia.
Pieter’s project is a good example of the application of scien-
tific methods in biology.

Biology is the scientific study of living things. Biologists
study processes from the level of molecules to the level of en-
tire ecosystems. They study events that happen in millionths
of seconds and events that occur over millions of years. Biol-
ogists ask many different kinds of questions and use a wide
range of tools, but they all use the same scientific methods.
Their goals are to understand how organisms (and assem-
blages of organisms) function, and to use that knowledge to
help solve problems.
In this chapter, we will take a closer look at what biologists
do. First, we will describe the characteristics of living things,
the major evolutionary events that have occurred during the
history of life on Earth, and the evolutionary tree of life. Then
we will discuss the methods biologists use to investigate how
life functions. At the end of the chapter, we will discuss how
scientific knowledge is used to shape public policy.
What Is Life?
Before we probe more deeply into the study of life, we need
to agree on what life is. Although we all know a living thing
when we see one, it is difficult to define life unambiguously.
One concise definition of life is: an organized genetic unit ca-
pable of metabolism, reproduction, and evolution. Much of this
book is devoted to describing these characteristics of life and
how they work together to enable organisms to survive and
reproduce (Figure 1.1). The following brief overview will
guide your study of these characteristics.
Metabolism involves conversions
of matter and energy
Metabolism, the total chemical activity of a living organism,
consists of thousands of individual chemical reactions.

Chemical reactions result in the capture of matter and energy
and its conversion to different forms, as we will see in Part
One of this book. For an organism to function, these reac-
tions, many of which are occurring simultaneously, must be
coordinated. Genes provide that control. The nature of the
genetic material that controls these lifelong events has been
understood only within the last 100 years. Much of Part Two
is devoted to the story of its discovery.
The external environment can change rapidly and unpre-
dictably in ways that are beyond an organism’s control. An
organism can remain healthy only if its internal environment
remains within a given range of physical and chemical con-
ditions. Organisms maintain relatively constant internal en-
2 CHAPTER ONE
1.1 The Many Faces of a Life The caterpillar,pupa, and adult are
all stages in the life cycle of a monarch butterfly (Danaeus plexippus).
The caterpillar harvests the matter and energy needed to metabolize
the millions of chemical reactions that will result in its growth and
transformation,first into a pupa and finally into an adult butterfly
specialized for reproduction and dispersal.The transition from one
stage to another is triggered by internal chemical signals.
vironments by making metabolic adjustments to conditions
such as changes in temperature, the presence or absence of
sunlight, or the presence of foreign agents inside their bodies.
Maintenance of a relatively stable internal condition, such as
a human’s constant body temperature, is called homeostasis.
The adjustments that organisms make to maintain home-
ostasis are usually not obvious, because nothing appears to
change. However, at some time during their lives, many or-
ganisms respond to changing conditions not by maintaining

their status, but by undergoing a major reorganization. An
early form of such reorganization was the evolution of rest-
ing spores, a well protected, inactive form in which organisms
survived stressful environments. A striking example that
evolved much later is seen in many insects, such as butterflies.
In response to internal chemical signals, a caterpillar changes
into a pupa and then into an adult butterfly (see Figure 1.1).
Reproduction continues life and provides
the basis for evolution
Reproduction with variation is a major characteristic of life.
Without reproduction, life would quickly come to an end.
The earliest single-celled organisms reproduced by duplicat-
ing their genetic material and then dividing in two. The two
resulting daughter cells were identical to each other and to
the parent cell, except for mutations that occurred during the
process of gene duplication. Such errors, although rare, pro-
vided the raw material for biological evolution. The combi-
nation of reproduction and errors in the duplication of ge-
netic material results in biological evolution, a change in the
genetic composition of a population of organisms over time.
The diversification of life has been driven in part by vari-
ation in the physical environment. There are cold places and
warm places, as well as places that are cold during some
parts of the year and warm during other parts. Some places
(oceans, lakes, rivers) are wet; others (deserts) are usually
very dry. No single kind of living thing can perform well in
all these environments. In addition, living things generate
their own diversity. Once plants evolved, they became a
source of food for other living things. Eaters of plants were,
in turn, potential food for other organisms. And when living

things die, they become food for still other organisms. The
differences among living things that enable them to live in
different kinds of environments and adopt different lifestyles
are called adaptations. The great diversity of living things
contributes to making biology a fascinating science and Earth
a rich and rewarding place to live.
For a long period of time, there was no life on Earth. Then
there was an extended period of only unicellular life, fol-
lowed by a proliferation of multicellular life. In other words,
the nature and diversity of life has changed over time. Iden-
tification of the processes that result in biological evolution
was one of the great scientific advances of the nineteenth
century. These processes will be discussed in detail in Part
Four of this book. Here we will briefly describe how they
were discovered.
Biological Evolution:
Changes over Billions of Years
Long before the mechanisms of biological evolution were un-
derstood, some people realized that organisms had changed
over time and that living organisms had evolved from or-
ganisms that were no longer alive on Earth. In the 1760s, the
French naturalist Count George-Louis Leclerc de Buffon
(1707–1788) wrote his Natural History of Animals, which con-
tained a clear statement of the possibility of evolution. Buffon
observed that the limb bones of all mammals were remark-
ably similar in many details (Figure 1.2). He also noticed that
the legs of certain mammals, such as pigs, have toes that
never touch the ground and appear to be of no use. He found
it difficult to explain the presence of these seemingly useless
small toes by the commonly held belief that Earth and all its

creatures had been divinely created in their current forms rel-
atively recently. To explain these observations, Buffon sug-
gested that the limb bones of mammals might all have been
inherited from a common ancestor, and that pigs might have
functionless toes because they inherited them from ancestors
that had fully formed and functional toes.
AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 3
Bones of the same type are shown in the same color.
Human arm Dog foreleg Seal flipper
1.2 All Mammals Have Similar Limbs Mammalian forelimbs have
different purposes:Humans use theirs for manipulating objects, dogs
use theirs for walking,and seals use theirs for swimming.But the
numbers and types of their bones are similar, indicating that they
have been modified over time from the forelimbs of a common
ancestor.
Buffon did not attempt to explain how such changes took
place, but his student Jean-Baptiste de Lamarck (1744–1829)
proposed a mechanism for such changes. Lamarck suggested
that a lineage of organisms could change gradually over
many generations as offspring inherited structures that
had become larger and more highly developed as a result of
continued use or, conversely, had become smaller and less
developed as a result of lack of use. Today scientists do not
believe that evolutionary changes are produced by this mech-
anism. But Lamarck had made an important effort to explain
how living things change over time.
Darwin provided a mechanistic explanation
of biological evolution
By 1858, the climate of opinion (among many biologists,
at least) was receptive to a new theory of evolutionary

processes proposed independently by Charles Darwin and
Alfred Russel Wallace. By that time, geologists had accumu-
lated evidence that Earth had existed and changed over mil-
lions of years, not merely a few thousand years, as most peo-
ple had previously believed.
You will learn more about Darwin’s theory of evolution
by natural selection in Chapter 23, but its essential features
are simple. You will need to be familiar with these ideas to
understand the rest of this book. Darwin’s theory rests on
three observations and one conclusion he drew from them.
The three observations are:

The reproductive rates of all organisms, even slowly
reproducing ones, are sufficiently high that populations
would quickly become enormous if death rates were not
equally high.

Within each type of organism, there are differences
among individuals.

Offspring are similar to their parents because they inher-
it their parents’ features.
Based on these observations (evidence), Darwin drew the
following conclusion:

The differences among individuals influence how well
those individuals survive and reproduce. Any traits that
increase the probability that their bearers will survive
and reproduce are passed on to their offspring and to
their offspring’s offspring.

Darwin called the differential survival and reproductive suc-
cess of individuals natural selection. He called the resulting
pattern “descent with modification.”
Biologists began a major conceptual shift a little more than
a century ago with the acceptance of long-term evolutionary
change and the gradual recognition that natural selection is
the process that adapts organisms to their environments. The
shift has taken a long time because it required abandoning
many components of an earlier worldview. The pre-Darwin-
ian view held that the world was young, and that organisms
had been divinely created in their current forms. In the Dar-
winian view, the world is ancient, and both Earth and its in-
habitants have changed over time. Ancestral forms were very
different from the organisms that exist today. Living organ-
isms evolved their particular features because ancestors with
those features survived and reproduced more successfully
than did ancestors with different features.
Major Events in the History of Life on Earth
The history of life on Earth, depicted on the scale of a 30-day
calendar, is outlined in Figure 1.3. The profound changes that
have occurred over the 4 billion years of this history are the
result of natural processes that can be identified and studied
using scientific methods. In this section, we will set the stage
for the rest of this book by describing some of the most
important of these changes. These six major evolutionary
events will provide us with a framework for discussing both
life’s characteristics and how those characteristics evolved.
By recognizing them, you will be able to better appreciate
both the unity and diversity of life.
Life arose from nonlife via chemical evolution

The first life must have come from nonlife. All matter, living
and nonliving, is made up of chemicals. The smallest chemi-
cal units are atoms, which bond together into molecules (the
properties of these units are the subject of Chapter 2). The
processes of chemical evolution that led to the appearance of
life began nearly 4 billion years ago, when random inorganic
chemical interactions produced molecules that had the re-
markable property of acting as templates to form similar mol-
ecules. Some of the chemicals involved may have come to
Earth from space, but chemical evolution continued on Earth.
The information stored in these simple molecules enabled
the synthesis of larger molecules with complex but relatively
stable shapes. Because they were both complex and stable,
these molecules could participate in increasing numbers and
kinds of chemical reactions. Certain types of large molecules
are found in all living systems; the properties and functions
of these complex molecules are the subject of Chapter 3.
Biological evolution began when cells formed
About 3.8 billion years ago, interacting systems of molecules
came to be enclosed in compartments. Within those units—
cells—control was exerted over the entrance, retention, and
exit of molecules, as well as over the chemical reactions tak-
ing place. The origin of cells marked the beginning of bio-
4 CHAPTER ONE
logical evolution. Cells and the membranes that enclose them
are the subjects of Chapters 4 and 5.
Cells are so effective at capturing energy and replicating
themselves—two fundamental characteristics of life—that
since they evolved, cells have been the unit on which all life is
built. Experiments by the French chemist and microbiologist

Louis Pasteur and other scientists during the nineteenth cen-
tury (described in Chapter 3) convinced most scientists that,
under present conditions on Earth, cells do not arise from non-
cellular material, but come only from other cells.
For 2 billion years after cells originated, all organisms were
unicellular (had only one cell). They were confined to the
oceans, where they were shielded from lethal ultraviolet
light. These simple cells, called prokaryotic cells, had no in-
ternal membrane-enclosed compartments.
Photosynthesis changed the course of evolution
A major event that took place about 2.5 billion years ago was
the evolution of photosynthesis: the ability to use the energy
of sunlight to power metabolism. All cells must obtain raw
materials and energy to fuel their metabolism. Photosynthetic
cells take up raw materials from their environment, but the en-
ergy they use to metabolize those chemicals comes directly
from the sun. Early photosynthetic cells were probably simi-
lar to present-day prokaryotes called cyanobacteria (Figure 1.4).
The energy-capturing process they used, which we will de-
scribe in Chapter 8, is the basis of nearly all life on Earth today.
Oxygen gas (O
2
) is a by-product of photosynthesis. Once
photosynthesis evolved, photosynthetic prokaryotes became
so abundant that they released vast quantities of O
2
into the
atmosphere. The O
2
we breathe today would not exist with-

out photosynthesis. When it first appeared in the atmos-
phere, however, O
2
was poisonous to most organisms then
living on Earth. Those prokaryotes that evolved a tolerance
to O
2
were able to successfully colonize en-
vironments emptied of other organisms and
proliferate in great abundance. For those
prokaryotes, the presence of oxygen opened
up new avenues of evolution. Metabolic re-
actions that use O
2
, called aerobic metabolism,
are more efficient than the anaerobic (non-
oxygen-using) metabolism that earlier
prokaryotes had used. Aerobic metabolism
allowed cells to grow larger, and it came to
be used by most organisms on Earth.
Over a much longer time frame, the vast
quantities of oxygen released by photosyn-
thesis had another effect. Formed from O
2
,
ozone (O
3
) began to accumulate in the up-
per atmosphere. The ozone slowly formed
a dense layer that acted as a shield, inter-

AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 5
27
First life?
12
6
39
27 28 29 30
Each “day” represents
about 150 million years.
Life appeared some time during “days”
3–4, or about 4 billion years ago.
Homo sapiens (modern
humans) appeared in the
last 10 minutes of day 30.
Recorded history
fills the last 5
seconds of day 30.
1.3 Life’s Calendar If the history of life on
Earth is “drawn”as a 30-day calendar,recorded
human history takes up only the last 5 seconds.
1.4 Oxygen Produced by Prokaryotes Changed Earth’s
Atmosphere This modern cyanobacterium may be very similar to
early photosynthetic prokaryotes.
cepting much of the sun’s deadly ultraviolet radiation. Even-
tually (although only within the last 800 million years of evo-
lution), the presence of this shield allowed organisms to leave
the protection of the ocean and establish new lifestyles on
Earth’s land surfaces.
Cells with complex internal compartments arose
As the ages passed, some prokaryotic cells became large

enough to attack, engulf, and digest smaller prokaryotes, be-
coming the first predators. Usually the smaller cells were de-
stroyed within the predators’ cells, but some of these smaller
cells survived and became permanently integrated into the
operation of their host cells. In this manner, cells with com-
plex internal compartments, called eukaryotic cells, arose.
The hereditary material of eukaryotic cells is contained
within a membrane-enclosed nucleus and is organized into
discrete units. Other compartments are specialized for other
purposes, such as photosynthesis (Figure 1.5).
Multicellularity arose and cells became specialized
Until slightly more than 1 billion years ago, only unicellular
organisms (both prokaryotic and eukaryotic) existed. Two
key developments made the evolution of multicellular organ-
isms—organisms consisting of more than one cell—possible.
One was the ability of a cell to change its structure and func-
tioning to meet the challenges of a changing environment.
This was accomplished when prokaryotes evolved the abil-
ity to transform themselves from rapidly growing cells into
resting spores that could survive harsh environmental con-
ditions. The second development allowed cells to stick to-
gether after they divided and to act together in a coordinated
manner.
Once organisms began to be composed of many cells, it
became possible for the cells to specialize. Certain cells, for
example, could be specialized to perform photosynthesis.
Other cells might become specialized to transport raw mate-
rials, such as water and nitrogen, from one part of an organ-
ism to another.
Sex increased the rate of evolution

The earliest unicellular organisms reproduced by dividing,
and the resulting daughter cells were identical to the parent
cell. But sexual recombination—the combining of genes from
two different cells in one cell—appeared early during the
evolution of life. Early prokaryotes engaged in sex (ex-
changes of genetic material) and reproduction (cell division)
at different times. Even today in many unicellular organisms,
sex and reproduction are separated in time.
Simple nuclear division—mitosis—was sufficient for the
reproductive needs of most unicellular organisms, and gene
exchange (a separate event) could occur at any time. Once or-
ganisms came to be composed of many cells, however, cer-
tain cells began to be specialized for sex. Only these special-
ized sex cells, called gametes, could exchange genes, and the
sex lives of multicellular organisms became more compli-
cated. A whole new method of nuclear division—meiosis—
evolved. An intricate and complex process, meiosis opened
up a multitude of possibilities for genetic recombination be-
tween gametes. Mitosis and meiosis are explained and com-
pared in Chapter 9.
Sex increased the rate of evolution because an organism
that exchanges genetic information with another individual
produces offspring that are more genetically variable than
the offspring of an organism that reproduces by mitotic di-
vision of its own cells. Some of these varied offspring are
likely to survive and reproduce better than others in a vari-
able and changing environment. It is this genetic variation
that natural selection acts on.
Levels of Organization of Life
Biology can be visualized as a hierarchy of units, ordered

from the smallest to the largest. These units are molecules,
cells, tissues, organs, organisms, populations, communities,
and the biosphere (Figure 1.6).
The organism is the central unit of study in biology; Parts
Six and Seven of this book discuss organismic biology in de-
tail. But to understand organisms, biologists study life at all
its levels of organization. They study molecules, chemical re-
actions, and cells to understand the functioning of tissues and
organs. They study organs and organ systems to determine
how organisms maintain homeostasis. At higher levels in the
hierarchy, biologists study how organisms interact with one
6 CHAPTER ONE
Nucleus
Eukaryotic cells contain many
membrane-enclosed compartments,
known as organelles.
1.5 Multiple Compartments Characterize Eukaryotic Cells The
nucleus and other specialized compartments of eukaryotic cells
evolved from small prokaryotes that were ingested by larger pro-
karyotic cells.
another to form social systems, populations, and ecological
communities, which are the subjects of Part Eight of this book.
The Evolutionary Tree of Life
All organisms on Earth today are the descendants of a single
kind of unicellular organism that lived almost 4 billion years
ago. But if that were the whole story, only one kind of or-
ganism might exist on Earth today. Instead, Earth is popu-
lated by many millions of different kinds of organisms that
do not interbreed with one another. We call these genetically
independent kinds species.

Why are there so many species? As long as individuals
within a population mate at random and reproduce, struc-
tural and functional changes may evolve within that popu-
lation, but only one species will exist. However, if a popula-
tion becomes separated and isolated into two or more
groups, individuals within each group will mate only with
one another. When this happens, structural and functional
differences between the groups may accumu-
late over time, and the groups may evolve
into different species. The splitting of groups
of organisms into separate species has re-
sulted in the great diversity of life found on
Earth today. The ways in which species form
are explained in Chapter 24.
Sometimes humans refer to a species as
“primitive” or “advanced.” These and similar
terms, such as “lower” and “higher,” are best
avoided in biology because they imply that
some organisms function better than others.
In fact, all living organisms are successfully
adapted to their environments. The shape and
strength of a bird’s beak, or the form and dis-
persal mechanisms of a plant’s seeds are ex-
amples of the rich array of adaptations found
among living organisms (Figure 1.7). The
abundance and success of prokaryotes—all of
which are relatively simple organisms—read-
ily demonstrates that they are highly func-
tional. In this book, we use the terms simple
and complex to refer to the level of complexity

of a particular organism. We use the terms an-
cestral and derived to distinguish characteris-
tics that appeared earlier from those that ap-
peared later in evolution.
As many as 30 million species of organ-
isms may live on Earth today. Many times
that number lived in the past, but are now ex-
AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 7
Molecules are made up of
atoms, and in turn can be
organized into cells.
A tissue is a group of many
cells with similar and
coordinated functions.
Atoms
Molecule
Cell (neuron)
Tissue (ganglion)
Organ (brain)
Organism (fish)
Population (school of fish)
An organism is a recognizable, self-
contained individual made up of
organs and organ systems.
Communities consist of
populations of many
different species.
Biosphere
A population is a group of many
organisms of the same species.

Community (coral reef)
Biological communities exchange
energy with one another, combining
to create the biosphere of Earth.
Cells of many types are the
working components of
living organisms.
Organs combine several tissues that
function together. Organs form
systems, such as the nervous system.
1.6 From Molecules to the Biosphere:The Hierarchy of Life
tinct. This diversity is the result of millions of splits in popu-
lations, known as speciation events. The unfolding of these
events can be expressed as an evolutionary “tree” showing
the order in which populations split and eventually evolved
into new species (see Figure 1.8). An evolutionary tree, with
its “trunk” and its increasingly finer “branches,” traces the
descendants coming from ancestors that lived at different
times in the past. That is, a tree shows the evolutionary rela-
tionships among species and groups of species. The organ-
isms on any one branch share a common ancestor at the base
of that branch. The most closely related groups are together
on the same branch. More distantly related organisms are on
different branches. In this book, we adopt the convention that
time flows from left to right, so the tree in Figure 1.8 (and
other trees in this book) lies on its side, with its root—the an-
cestor of all life—at the left.
The U.S. National Science Foundation is sponsoring a ma-
jor initiative, called Assembling the Tree of Life (ATOL). Its
goal is to determine the evolutionary relationships among all

species on Earth. Achieving this goal is possible today be-
cause, for the first time, biologists have the technology to as-
semble the complete tree of life, from microbes to mammals.
Data for ATOL come from a variety of sources. Fossils—the
preserved remains of organisms that lived in the past—tell
us where and when ancestral organisms lived and what they
may have looked like. With modern molecular genetic tech-
niques such as DNA sequencing, we can determine how
many genes different species share, and information tech-
8 CHAPTER ONE
(a)
(b)
The strong, curved beak of the bald
eagle is able to tear the flesh from
large fish and other sizeable prey.
The curlew uses its long, curved, pointed
beak to extract small crustaceans from
the surface of mud, sand, and soil.
The roseate spoonbill moves
its bill through the water, from
which it filters food items.
The coconut seed is covered by a
thick husk that protects it as it drifts
across thousands of miles of ocean.
Mammals and birds eat
blackberries, then
disseminate the seeds
when they defecate.
The seeds of milkweeds are
surrounded by “kites” of fibers that

carry them on wind currents.
1.7 Adaptations to the Environment (a) Bird beaks are adapted
to specific types of food items.(b) Plants cannot move, but their seeds
have adaptations that allow them to travel varying distances from
the parent plant.
nology enables us to synthesize masses of genetic data. The
ATOL initiative, one of the grandest projects of modern biol-
ogy, is projected to take at least two decades and to involve
hundreds of scientists working in a diverse array of fields.
The reason it will take so long to complete is that most of
Earth’ species have not yet been described.
The Tree of Life will be an information framework for bi-
ology in much the same way that the periodic table of ele-
ments is an information framework for chemistry and
physics. Evolution has conducted several billion years of free
research and development. Every living thing carries a ge-
netic “package” that has been tested by natural selection. Sci-
entists can now unwrap and study these packages, learning
much about the processes that produced them.
Although much remains to be accomplished, biologists
know enough to have assembled a provisional tree of life, the
broad outlines of which are shown in Figure 1.8. The branch-
ing patterns of this tree are based on a rich array of evidence,
but no fossils are available to help us determine the earliest
divisions in the lineages of life because those simple organ-
isms had no parts that could be preserved as fossils. There-
fore, molecular evidence has been used to separate all living
organisms into three major domains. Organisms belonging
to a particular domain have been evolving separately from
organisms in the other domains for more than a billion years.

Organisms in the domains Archaea and Bacteria are
prokaryotes. Archaea and Bacteria differ so fundamentally
from one another in their metabolic processes that they are be-
lieved to have separated into distinct
evolutionary lineages very early dur-
ing the evolution of life. These two do-
mains are described in Chapter 27.
Members of the other domain—
Eukarya—have eukaryotic cells. The
Eukarya are divided into four groups:
Protista, Plantae, Fungi, and Animalia.
The Protista (protists), the subject of
Chapter 28, contains mostly single-
celled organisms. The other three
groups, referred to as kingdoms, are be-
lieved to have arisen from ancestral
protists. All of their members are mul-
ticellular.
Some bacteria, some protists, and
most members of the kingdom Plantae
(plants) convert light energy to chem-
ical energy by photosynthesis. These
organisms are called autotrophs (“self-feeders”). The biological
molecules they produce are the primary food for nearly all
other living organisms. The kingdom Plantae is covered in
Chapters 29 and 30.
The kingdom Fungi, the subject of Chapter 31, includes
molds, mushrooms, yeasts, and other similar organisms, all
of which are heterotrophs (“other-feeders”)—that is, they re-
quire a source of energy-rich molecules synthesized by other

organisms. Fungi break down food molecules in their envi-
ronment and then absorb the breakdown products into their
cells. They are important as decomposers of the dead mate-
rials of other organisms.
Members of the kingdom Animalia (animals) are het-
erotrophs that ingest their food source, digest the food out-
side their cells, and then absorb the breakdown products. An-
imals eat other forms of life to obtain their raw materials and
energy. This kingdom is covered in Chapters 32, 33, and 34.
We will discuss the principal levels used in today’s clas-
sification scheme for living organisms in Chapter 25. But to
understand some of the terms we will use in the interven-
ing chapters, you need to know that each species of organ-
ism is identified by two Latinized names (a binomial). The
first name identifies the genus—a group of species that
share a recent common ancestor—of which the species is a
member. The second name is the species name. To avoid
confusion, no combination of two names is assigned to more
than one species. For example, the scientific name of the hu-
man species is Homo sapiens: Homo is our genus and sapiens is
our species. The Pacific tree frogs Pieter Johnson studied are
called, in scientific nomenclature, Hyla regilla.
Biology is the study of all of Earth’s organisms, both those
living today and those that lived in the past, so even extinct
species are given binomials. These unique and exact names
AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 9
PresentAncient
Time
Archaea and
Eukarya share a

common ancestor
not shared by
bacteria.
There are multiple protist
lineages. Plants, fungi, and
animals are descended from
different protist ancestors.
Protists
Animalia
Fungi
Plantae
Protists
Protists
Archaea
Bacteria
Common
ancestor of
all organisms
BACTERIA
ARCHAEA
EUKARYA
1.8 A Provisional Tree of Life The classification system
used in this book divides Earth’s organisms into three
domains; Bacteria, Archaea, and Eukarya. Protists are descen-
dants of multiple ancestors.
illuminate the tremendous diversity of life, and are im-
portant tools for biologists because, as in all the sciences,
precise and unambiguous communication of research infor-
mation is critical.
Biology Is a Science

To study the rich variety of living things, biologists employ
many different methods. Direct observations by unaided
senses are central to many scientific investigations, but sci-
entists also use many tools that augment the human senses.
For example, to study objects that are too small to be seen
with the unaided eye, scientists use microscopes. To observe
and magnify remote objects, scientists use telescopes. To
study events that happened thousands to millions of years
ago, scientists “read” radioactive isotopes of chemical ele-
ments that decay at specific rates.
Conceptual tools guide scientific research
In addition to such technical tools, scientists use a variety of
conceptual tools to help them answer questions about nature.
The method that underlies most scientific research is the
hypothesis-prediction (H–P) approach. The H–P approach
allows scientists to modify their conclusions as new infor-
mation becomes available. The method has five steps:
1. Making observations
2. Asking questions
3. Forming hypotheses, which are tentative answers to the
questions
4. Making predictions based on the hypotheses
5. Testing the predictions by making additional observa-
tions or conducting experiments
If the results of the testing support the hypothesis, it is sub-
jected to additional predictions and tests. If they continue to
support it, confidence in its correctness increases, and the hy-
pothesis comes to be considered a theory. If the results do not
support the hypothesis, it is abandoned or modified in ac-
cordance with the new information. Then new predictions

are made, and more tests are conducted.
Hypotheses are tested in two major ways
Tests of hypotheses are varied, but most are of two types:
controlled experiments and the comparative method. When
possible, scientists use controlled experiments to test pre-
dictions from hypotheses. That is what Pieter Johnson was
doing when he hatched frog eggs in the laboratory. He pre-
dicted that if his hypothesis—that the parasite Ribeiroia
caused deformities in frogs—was correct, then frogs raised
with the parasite would develop deformities and frogs raised
in the absence of the parasite would not. The advantage of
controlled experiments is that all factors other than the one hy-
pothesized to be causing the effect can be kept constant; that is, any
other factors that might influence the outcome (such as wa-
ter temperature and pH in Pieter’s experiment) are con-
trolled. The most powerful experiments are those that have
the ability to demonstrate that the hypothesis or the predic-
tions made from it are wrong.
But many hypotheses cannot be tested with controlled ex-
periments. Such hypotheses are tested by making predic-
tions about patterns that should exist in nature if the hy-
pothesis is correct. Data are then gathered to determine
whether those patterns in fact do exist. This approach is
called the comparative method. It is the primary approach
of scientists in some fields, such as astronomy, in which ex-
periments are rarely possible. Biologists regularly use the
comparative method.
A single piece of supporting evidence rarely leads to wide-
spread acceptance of a hypothesis. Similarly, a single contrary
result rarely leads to abandonment of a hypothesis. Results

that do not support the hypothesis can be obtained for many
reasons, only one of which is that the hypothesis is wrong.
For example, incorrect predictions can be made from a cor-
rect hypothesis. Poor experimental design, or the use of an
inappropriate organism, can also lead to erroneous results.
We will now show how the H–P method was used by
other researchers to investigate the larger question that con-
cerned Pieter Johnson: Why are amphibian populations de-
clining dramatically in many places on Earth?
STEP 1: MAKING OBSERVATIONS. Amphibian populations,
like populations of most organisms, fluctuate over time.
Before we decide that the current declines are different
from “normal” population fluctuations, we first need to
establish that they are unusual. To assess whether the cur-
rent declines are unusual, an international group of scien-
tists has been gathering worldwide data on amphibian
populations. The group’s data show that amphibian popu-
lations are declining seriously in some parts of the world,
especially western North America, Central America, and
northeastern Australia, but not others, such as the Amazon
Basin. Their data also show that population declines are
greater in mountains than in adjacent lowlands. These sci-
entists also discovered that no data on population trends in
amphibians are available from Africa or Asia.
STEP 2: ASKING QUESTIONS. Two questions were suggested
by these observations: Why are amphibian declines greater
at high elevations? Why are amphibians declining in some
regions, but not in others?
10 CHAPTER ONE
STEPS 3 AND 4: FORMULATING HYPOTHESES AND MAKING PREDIC-

TIONS
. To develop hypotheses about the first question, sci-
entists first identified the environmental factors that change
with elevation. Temperatures drop and rainfall increases
with elevation worldwide, and in temperate regions, sum-
mer levels of ultraviolet-B (UV-B) radiation increase about
18 percent per 1,000 meters of elevation gain. One hypothe-
sis is that declines in the populations of some amphibian
species are due to global increases in UV-B radiation result-
ing from reductions in atmospheric ozone concentrations. If
increased levels of UV-B are adversely affecting amphibian
populations, we predict that experimentally reducing UV-B
over ponds where amphibian eggs are incubating and lar-
vae are developing should improve their survival.
STEP 5: TESTING HYPOTHESES. The hy-
pothesis that exposure to increased
levels of UV-B might contribute to
amphibian population decline was
tested by comparing the responses of
tadpoles of two species of frogs that
live in Australian mountains. One
species (Litoria verreauxii) had disap-
peared from high elevations; the other
(Crinia signifera) had not. Because at
higher elevations tadpoles are exposed
to higher levels of UV-B radiation, ex-
perimenters predicted that L. verreauxii
would survive less well than C. sig-
nifera if exposed to UV-B radiation typ-
ical of high elevations (Figure 1.9).

As predicted, when exposed to UV-B
radiation, individuals of C. signifera sur-
vived well, but all individuals of L. ver-
reauxii died within two weeks. Among
control populations raised in tanks cov-
ered by filters that blocked UV trans-
mission, individuals of both species sur-
vived well. Thus, the results supported
the hypothesis.
Figure 1.9 describes one of many experiments in which the
UV-B hypothesis has been tested. Some other experiments
have yielded similar results, while others have shown no ef-
fects of UV-B exposure, or have shown a negative effect of
UV-B exposure only when it is associated with low pH.
Several hypotheses have also been proposed to account
for regional differences in amphibian population declines, in-
cluding the adverse effects of habitat alteration by humans.
Two obvious forms of human habitat alteration are air pol-
lution from areas of urban and industrial growth, and the air-
borne pesticides used in agriculture.
A straightforward prediction from the habitat alteration hy-
pothesis is that amphibian declines should be more noticeable
in areas exposed to higher amounts of human-generated air
AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 11
RESULTS
EXPERIMENT
Conclusion: The results support the hypothesis that suceptibility to UV-B radiation has
contributed to the disappearance of Litoria verreauxii from high elevations.
Hypothesis: Susceptibility to UV-B radiation has contributed to the disappearance of some
frogs from high-elevation ponds.

The probability of dying was much greater for individuals of the species that
had disappeared from high elevations (Litoria verreauxii) than for individuals
of the species surviving there (Crinia signifera).
Probability of dying
5 10 15 20 25 30
Time (days)
0.5
(all die)
1.0
0.0
(all
survive)
Filtered, UV-B allowedUnfiltered sunlight Filtered, UV-B blocked
Crinia signifera
Probability of dying
5 10 15 20 25 30
Time (days)
0.5
1.0
0.0
Crinia signifera
5 10 15 20 25 30
Time (days)
Litoria verreauxii
5 10 15 20 25 30
Time (days)
Litoria verreauxii
Elevation 1,365 meters
Elevation 1,600 meters
METHOD

Establish 3 identical artificial tanks at each of 2 elevations (1,365 meters and
1,600 meters). Set up 6 trays in each tank. Place equal numbers of embryos of
one of the two frog species in each tray. In each tank, 2 trays receive unfiltered
sunlight; 2 receive sunlight filtered to remove UV-B; and 2 receive filtered
sunlight that allowed UV-B transmission. Count the number of surviving
individuals 3 times a week for 4 weeks.
1.9 A Controlled Experiment Tests the
Effects of UV-B The results of this experi-
ment suggest that UV-B susceptibility has
contributed to the decline of some amphib-
ian populations. Experimental populations of
both species were subjected to different lev-
els of UV radiation; the filtered-light popula-
tion (no UV-B exposure) acted as a control.
pollutants than in areas with less expo-
sure. This hypothesis has been tested us-
ing the comparative method. The exten-
sive tests compared population trends
in eight species of amphibians in the
state of California. The species studied
included four frog species of the genus
Rana, two species of toads, and a sala-
mander species. The bases of the tests
were simple censuses (surveys and
counts) to determine whether popula-
tions of a given species were present or
absent at each of the hundreds of study
sites across the state. The census results
for one of the eight species, the frog
Rana aurora, are shown in Figure 1.10.

The map in Figure 1.10 shows a sig-
nificant trend for R. aurora: Populations
of this amphibian are more likely to be
absent from sites downwind of large ur-
ban and agricultural areas (and thus ex-
posed to heavy airborne pollution), and
present in sites upwind (not heavily ex-
posed). This type of data is the basis of
the comparative method. In this partic-
ular study, meticulous tallying and com-
parison of similar data for all eight
species showed that some species ex-
hibited significant declines in exposed
areas, but others (including the toads),
did not. Therefore, we may conclude
that human habitat alteration could be
responsible for regional differences in
the declines of some species.
Other studies have addressed other
hypotheses about the decline of am-
phibian populations. Some evidence
indicates that smoke from extensive
fires also is adversely affecting am-
phibians. Climate change is clearly im-
portant in areas such as Central Amer-
ica, where a series of warm, dry years
during the breeding season may have
resulted in the extinction of Costa
Rica’s golden toad. And, as Pieter John-
son demonstrated, parasites are part of

the problem.
Even though much more information needs to be gath-
ered, it is already evident that no single factor is causing am-
phibian declines. This finding is not surprising, because no
two places on Earth are the same, and no two species of am-
phibians respond in exactly the same way to changes in the
environment. In their responses to environmental changes,
amphibians are like most living things. They live in complex
and changing environments, and they interact with many
other species.
12 CHAPTER ONE
COMPARATIVE METHOD
Conclusion: Airborne agricultural pesticides and urban air pollutants are contributing to
declines in populations of some amphibian species.
Hypothesis: Airborne pesticides from agricultural fields and urban air pollutants are
contributing to the decline of amphibian populations.
PREDICTION
If pesticides and urban air pollutants are factors in amphibian population
declines, populations close to and downwind from agricultural and
urban areas should have decreased more strikingly than populations
upwind and farther away from those sources of air pollutants.
Rana aurora present
Rana aurora absent
Average wind direction
Agriculture
RESULTS
METHOD
Census (count) and then compare persistence of populations of species of
amphibians at suitable habitat sites that lie upwind and downwind of
major agricultural and urban areas.

Populations of some species, as illustrated here by Rana aurora, persist in
areas upwind of or remote from sources of urban and agricultural
pollutants, but this amphibian is largely absent from areas close to or
downwind of air pollution sources. (Distributions of three other species
of Rana were similar to that of R. aurora.)
Upwind
Down-
wind
Urban area
San Francisco
Greater
Los Angeles
San Diego
Figure 1.10 Using the Comparative Method to Test a Hypothesis The effects of human-
generated airborne pollutants on amphibian populations can be assessed by determining
whether species persist in, or are absent from, suitable habitats that lie upwind or downwind
from sources of airborne pollutants.
Simple explanations that account for everything should not
be expected or trusted. Its complexities make biology a diffi-
cult science, but they also make it exciting and challenging.
Not all forms of inquiry are scientific
Scientific methods are the most powerful tools that humans
have developed to understand how the world works. Their
strength is founded on the development of hypotheses that
can be tested. The process is self-correcting because if the ev-
idence fails to support a hypothesis, it is either abandoned
or modified and subjected to further tests. In addition, be-
cause scientists publish detailed descriptions of the methods
they use to test hypotheses, other scientists can—and often
do—repeat those experiments. Therefore, any error or dis-

honesty usually is discovered. That is why, in contrast to
politicians, scientists around the world usually trust one an-
other’s results.
If you understand the methods of science, you can distin-
guish science from non-science. Art, music, and literature, ac-
tivities that contribute massively to the quality of human life,
are not science. They help us understand what it means to
live in a complex world. Religion is not science either. Reli-
gious beliefs give us meaning and spiritual guidance, and
they form a basis for establishing values. Scientific informa-
tion helps create the context in which values are discussed
and established, but it cannot tell us what those values
should be.
Biology has implications for public policy
The study of biology has long had major implications for hu-
man life. Agriculture and medicine are two important fields
of applied biology. People have been speculating about the
causes of diseases and searching for methods of combating
them since ancient times. Today, with the deciphering of the
genetic code and the ability to manipulate the genetic con-
stitution of organisms, vast new possibilities exist for im-
provements in the control of human diseases and agricultural
productivity. At the same time, these capabilities have raised
important ethical and policy issues. How much and in what
ways should we tinker with the genetics of people and other
species? Does it matter whether organisms are changed by
traditional breeding experiments or by gene transfers? How
safe are genetically modified organisms in the environment
and in human foods?
Another reason for studying biology is to understand the

effects of the vastly increased human population on its envi-
ronment. Our use of renewable and nonrenewable natural re-
sources is putting stress on the ability of the environment to
produce the goods and services upon which our society de-
pends. Human activities are changing global climates, causing
the extinction of a large number of species, and resulting in the
spread of new human diseases and the resurgence of old ones.
For example, the rapid spread of SARS and West Nile virus
was facilitated by modern modes of transportation. Biological
knowledge is vital for determining the causes of these changes,
for devising wise policies to deal with them, and for drawing
attention to the marvelous diversity of living organisms that
provides goods and services for humankind and also enriches
our lives aesthetically and spiritually.
Biologists are increasingly called upon to advise govern-
mental agencies concerning the laws, rules, and regulations
by means of which society deals with the increasing number
of problems and challenges that have at least a partial bio-
logical basis. As we discuss these issues in many chapters of
this book, you will see that the use of biological information
is essential if wise public policies are to be established and
implemented.
Throughout this book we will share with you the excite-
ment of studying living things and illustrate the rich array of
methods that biologists use to determine why the world of liv-
ing things looks and functions as it does. The most important
motivator of most biologists is curiosity. People are fascinated
by the richness and diversity of life and want to learn more
about organisms and how they interact with one another.
Humans probably evolved to be curious because individ-

uals who were motivated to learn about their surroundings
were likely to have survived and reproduced better, on aver-
age, than their less curious relatives. In other words, curios-
ity is adaptive! There are vast numbers of questions for which
we do not yet have answers, and new discoveries usually en-
gender questions no one thought to ask before. Perhaps your
curiosity will lead to an important new idea.
Chapter Summary
What Is Life?

Life can be defined as an organized genetic unit capable of
metabolism, reproduction, and evolution.

Metabolism, the total chemical activity of a living organism,
is controlled by genes.

Biological evolution is a change in the genetic composition
of a population of organisms over time.
Biological Evolution: Changes over Billions of Years

Charles Darwin’s theory of natural selection rests on three
simple observations and one conclusion drawn from them:
Any heritable traits that increase the probability that their bear-
ers will survive and reproduce are passed on to their offspring.
Review Figure 1.2
Major Events in the History of Life on Earth

Life arose from nonlife about 4 billion years ago by means of
chemical evolution. Review Figure 1.3
AN EVOLUTIONARY FRAMEWORK FOR BIOLOGY 13


Biological evolution began about 3.8 billion years ago when
interacting systems of molecules became enclosed in mem-
branes to form cells.

Photosynthetic prokaryotes released large amounts of oxygen
into Earth’s atmosphere, making aerobic metabolism possible.

Complex eukaryotic cells evolved by incorporation of smaller
cells that survived being ingested.

Multicellular organisms appeared when cells evolved the
ability to transform themselves and to stick together and com-
municate after they divided. The individual cells of multicellu-
lar organisms became modified to carry out varied functions
within the organism.

The evolution of sex sped up rates of biological evolution.
Levels of Organization of Life

Life is organized hierarchically, from molecules to the bios-
phere. Review Figure 1.6. See Web/CD Activity 1.1
The Evolutionary Tree of Life

A major effort called Assembling the Tree of Life (ATOL) is
underway to determine the evolutionary relationships among
all species on Earth.

The hierarchy of evolutionary relationships can be represent-
ed as an evolutionary tree. Review Figure 1.8. See Web/CD

Activity 1.2

Species are grouped into three domains: Archaea, Bacteria,
and Eukarya. The domains Archaea and Bacteria consist of
prokaryotic cells. The domain Eukarya contains the Protists,
Plantae, Fungi, and Animalia.
Biology Is a Science

Biologists use a variety of technical and conceptual tools to
study living things.

The hypothesis-prediction (H–P) approach is used in most
biological investigations. Hypotheses are tentative answers to
questions. Predictions are made on the basis of a hypothesis.
The predictions are tested by experiments and comparative
observations. Review Figures 1.9 and 1.10

Science can tell us how the world works, but it does not form
the basis for establishing meaning and values.

Biologists are often called upon to advise governmental agen-
cies on the solution of important problems that have a biological
component.
For Discussion
1. The information Darwin used to develop his theory of evo-
lution by natural selection was well known to his contem-
poraries. Why was it so difficult for people to think of such
an obvious mechanism of evolutionary change?
2. According to the theory of evolution by natural selection, a
species evolves certain features because they improve the

chances that its members will survive and reproduce. There
is no evidence, however, that evolutionary mechanisms
have foresight or that organisms can anticipate future condi-
tions. What, then, do biologists mean when they say, for
example, that wings are “for flying”?
3. The first organisms appeared nearly 4 billion years ago, but
multicellular organisms were slow to appear. Why did the
evolution of multicellularity take so long?
4. Why is it so important in science that we design and per-
form tests capable of falsifying a hypothesis?
5. What features characterize questions that can be answered
only by using a comparative approach?
6. Experiments show that not all amphibian declines are
caused by a single factor. Does this surprise you? What
kinds of environmental factors might be capable of affecting
amphibian populations everywhere on Earth? What factors
are likely to act only locally?
14 CHAPTER ONE
Mars today is a cold, dry place, not suitable for life as we know it.
But 3 billion years ago, it was warmer and wetter. An orbiting probe
from Earth recently photographed a huge dry lake bed, the size of
New Mexico and Texas combined, on the Martian surface. Another
probe found evidence of water trapped just below the icy surface of
the Martian polar region. These discoveries by geologists have sparked the interest
of biologists, for where there is water, there can be life. There is good reason to be-
lieve that life as we know it cannot exist without water.
Animals and plants that live on Earth’s land masses had to evolve elaborate ways
to retain the water that makes up about 70 percent of their bodies. Aquatic organisms
living in water do not need these water-retention mechanisms; thus biologists have
concluded that the first living things originated in a watery environment. This envi-

ronment need not have been the lakes, rivers, and oceans with which we are famil-
iar. Living organisms have been found in hot springs at temperatures above the usual
boiling point of water, in a lake beneath the frozen Antarctic ice, in water trapped 2
miles below Earth’s surface, in water 3 miles below the surface of the sea, in extremely
acid and extremely salty water, and even in the water that cools the interiors of nu-
clear reactors.
With 20 trillion galaxies in the universe, each with 100 billion stars, there are many
planets out there, and if our own solar system is typical, some of them have the wa-
ter needed for life. As biologists contemplate
how life could originate from nonliving mat-
ter, their attention focuses not just on the pres-
ence of water, but on what is dissolved in it.
A major discovery of biology is that living
things are composed of the same types of
chemical elements as the vast nonliving por-
tion of the universe. This mechanistic view—
that life is chemically based and obeys uni-
versal physicochemical laws—is a relatively
recent one in human history. The concept of a
“vital force” responsible for life, different from
the forces found in physics and chemistry, was
common in Western culture until the nine-
teenth century, and many people still assume
such a force exists. However, most scientists
adhere to a mechanistic view of life, and it is
the cornerstone of medicine and agriculture.
A Grander Canyon on Mars This false
color image from the Mars Global Surveyor
shows in blue the dry remains of what was
once a huge lake on Mars. Just as the

Colorado River carved Earth’s Grand
Canyon, torrents of water from the lake
probably carved the mile-deep canyon that
is visible as a thin blue line just north of the
lake bed.
Life and Chemistry: Small Molecules
2
Part One
•
THE CELL
16 CHAPTER TWO
Before describing how chemical elements are arranged in
living creatures, we will examine some fundamental chem-
ical concepts. We will first address the constituents of mat-
ter: atoms. We will examine their variety, their properties,
and their capacity to combine with other atoms. Then we
will consider how matter changes. In addition to changes in
state (solid to liquid to gas), substances undergo changes
that transform both their composition and their characteris-
tic properties. Then we will describe the structure and prop-
erties of water and its relationship to acids and bases. We
will close the chapter with a consideration of characteristic
groups of atoms that contribute specific properties to larger
molecules of which they are part, and which will be the sub-
ject of Chapter 3.
Water and the Origin of Life’s Chemistry
Astronomers believe our solar system began forming about
4.6 billion years ago when a star exploded and collapsed to
form the sun, and 500 or so bodies called planetesimals col-
lided with one another to form the inner planets, including

Earth. The first chemical signatures indicating the presence
of life here are about 4 billion years old. So it took 600 million
years, during a geological time frame called the Hadean, for
the chemical conditions on Earth to become just right for life.
Key among those conditions was the presence of water.
Ancient Earth probably had a lot of water high in the at-
mosphere. But the new planet was hot, and this water evap-
orated into space. As Earth cooled, it became possible for
water to remain on its surface, but where did that water
come from? One current view is that comets—loose ag-
glomerations of dust and ice that have orbited the sun since
the planets formed—struck Earth repeatedly and brought
not only water but other chemical components of life, such
as nitrogen. As Earth cooled, chemicals from the rocks dis-
solved in the water and simple chemical reactions took
place. Some of these reactions could have led to life, but im-
pacts by large comets and rocky meteorites would have re-
leased enough energy to heat the developing oceans almost
to boiling, thus destroying any early life. These large impacts
eventually subsided, and life gained a foothold about 3.8 to
4 billion years ago. The prebiotic Hadean was over (Figure
2.1). The Archean had begun, and there has been life on
Earth ever since.
In Chapter 3 we will return to the question of how the first
life could have arisen from inanimate chemicals. But before
doing so, we need to understand what the chemistry of life
entails. Like the rest of the chemical world, living things are
made up of atoms and molecules.
Atoms: The Constituents of Matter
More than a trillion (10

12
) atoms could fit over the period at
the end of this sentence. Each atom consists of a dense, pos-
itively charged nucleus, around which one or more nega-
tively charged electrons move (Figure 2.2). The nucleus con-
tains one or more protons and may contain one or more
neutrons. Atoms and their component particles have volume
and mass, which are properties of all matter. Mass measures
the quantity of matter present; the greater the mass, the
greater the quantity of matter.
The mass of a proton serves as a standard unit of measure:
the atomic mass unit (amu), or dalton (named after the Eng-
lish chemist John Dalton). A single proton or neutron has a
mass of about 1 dalton (Da), which is 1.7 × 10
–24
grams
(0.0000000000000000000000017 g). The mass of an electron is
9 × 10
–28
g (0.0005 Da). Because the mass of an electron is neg-
ligible compare to the mass of a proton or a neutron, the
4
3
2
1
Present
Billions of years ago
5
Phanerozoic: Current life
Proterozoic: More complex life

Archean: Early life
Hadean: Chemical evolution
Cambrian “explosion”
(see Chapter 22)
Atmospheric oxygen (O
2
)
Earliest life
Earth forms
2.1 A Geological Time Scale The Hadean encompasses the time
from the formation of Earth (about 4.6 billion years ago) until the earli-
est life appeared (about 3.8 billion years ago).During the Hadean
chemical conditions evolved that were conducive to life, which was
able to gain a foothold once the rain of comets and meteorites ended.
Each neutron has a mass
of 1 and no charge.
Each proton has a mass
of 1 and a positive charge.
Each electron has negligible
mass and a negative charge.
–
–
+
+
Nucleus
2.2 The Helium Atom This representation of a helium atom is
called a Bohr model. It exaggerates the space occupied by the
nucleus. In reality, although the nucleus accounts for virtually all of
the atomic mass,it occupies only 1/10,000 of the atom’s volume.
contribution of electrons to the mass of an atom can usually

be ignored when measurements and calculations are made.
It is electrons however, that determine how atoms will inter-
act in chemical reactions, and we will discuss them exten-
sively later in this chapter.
Each proton has a positive electric charge, defined as +1
unit of charge. An electron has a negative charge equal and
opposite to that of a proton; thus the charge of an electron is
–1 unit. The neutron, as its name suggests, is electrically neu-
tral, so its charge is 0 unit. Unlike charges (+/–) attract each
other; like charges (+/+ or –/–) repel each other. Atoms are
electrically neutral: The number of protons in an atom equals
the number of electrons.
An element is made up of only one kind of atom
An element is a pure substance that contains only one type
of atom. The element hydrogen consists only of hydrogen
atoms; the element iron consists only of iron atoms. The
atoms of each element have certain characteristics or prop-
erties that distinguish them from the atoms of other elements.
The more than 100 elements found in the universe are
arranged in the periodic table (Figure 2.3). These elements
are not found in equal amounts. Stars have abundant hy-
drogen and helium. Earth’s crust, and those of the neighbor-
ing planets, are almost half oxygen, 28 percent silicon, 8 per-
cent aluminum, 2–5 percent each of sodium, magnesium,
potassium, calcium, and iron, and contain much smaller
amounts of the other elements.
About 98 percent of the mass of every living organism (bac-
terium, turnip, or human) is composed of just six elements:
carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.
The chemistry of these six elements will be our primary con-

LIFE AND CHEMISTRY: SMALL MOLECULES 17
1
H
1.0079
3
Li
6.941
4
Be
9.012
11
Na
22.990
12
Mg
24.305
20
Ca
40.08
19
K
39.098
21
Sc
44.956
22
Ti
47.88
23
V

50.942
24
Cr
51.996
25
Mn
54.938
26
Fe
55.847
2
He
4.003
7
N
14.007
8
O
15.999
15
P
30.974
16
S
32.06
29
Cu
63.546
30
Zn

65.38
31
Ga
69.72
32
Ge
72.59
33
As
74.922
34
Se
78.96
35
Br
79.909
36
Kr
83.80
9
F
18.998
10
Ne
20.179
17
Cl
35.453
18
Ar

39.948
27
Co
58.933
28
Ni
58.69
5
B
10.81
6
C
12.011
13
Al
26.982
14
Si
28.086
37
Rb
85.4778
38
Sr
87.62
39
Y
88.906
40
Zr

91.22
41
Nb
92.906
42
Mo
95.94
43
Tc
(99)
44
Ru
101.07
47
Ag
107.870
48
Cd
112.41
49
In
114.82
50
Sn
118.69
51
Sb
121.75
52
Te

127.60
53
I
126.904
54
Xe
131.30
45
Rh
102.906
46
Pd
106.4
55
Cs
132.905
56
Ba
137.34
72
Hf
178.49
73
Ta
180.948
74
W
183.85
104
Rf

(261)
105
Db
(262)
106
Sg
(266)
107
Bh
(264)
108
Hs
(269)
109
Mt
(268)
110
(269)
111
(272)
112
(277)
113 114
(285)
115
(289)
116 117 118
(293)
75
Re

186.207
76
Os
190.2
79
Au
196.967
80
Hg
200.59
81
Tl
204.37
82
Pb
207.19
83
Bi
208.980
84
Po
(209)
85
At
(210)
86
Rn
(222)
77
Ir

192.2
78
Pt
195.08
87
Fr
(223)
88
Ra
226.025
58
Ce
140.12
59
Pr
140.9077
60
Nd
144.24
61
Pm
(145)
64
Gd
157.25
65
Tb
158.924
66
Dy

162.50
67
Ho
164.930
68
Er
167.26
69
Tm
168.934
70
Yb
173.04
62
Sm
150.36
63
Eu
151.96
90
Th
232.038
57
La
138.906
89
Ac
227.028
91
Pa

231.0359
92
U
238.02
93
Np
237.0482
96
Cm
(247)
97
Bk
(247)
98
Cf
(251)
99
Es
(252)
100
Fm
(257)
101
Md
(258)
102
No
(259)
71
Lu

174.97
94
Pu
(244)
95
Am
(243)
Lanthanide series
Actinide series
The six elements highlighted in
yellow make up 98% of the
mass of most living organisms.
Elements framed in orange
are present in small amounts
in many organisms.
Masses in parentheses indicate unstable elements
that decay rapidly to form other elements.
Elements without a chemical
symbol are as yet unnamed.
103
Lr
(260)
Vertical columns have elements
with similar properties.
–
–
+
+
2
He

4.003
Atomic number
(number of protons)
Chemical symbol
(for helium)
Atomic mass
(number of protons plus
number of neutrons
averaged over all isotopes)
2.3 The Periodic Table The periodic table groups
the elements according to their physical and chemi-
cal properties. Elements 1–92 occur in nature; ele-
ments above 92 were created in the laboratory.
18 CHAPTER TWO
cern here, but the others are not unimportant. Sodium and
potassium, for example, are essential for nerves to function;
calcium can act as a biological signal; iodine is a component of
a vital hormone; and plants need magnesium as part of their
green pigment (chlorophyll) and molybdenum in order to in-
corporate nitrogen into biologically useful substances.
The number of protons identifies the element
An element is distinguished from other elements by the num-
ber of protons in each of its atoms. This number, which does
not change, is called the atomic number. An atom of helium has
2 protons, and an atom of oxygen has 8 protons; the atomic
numbers of these elements are thus 2 and 8, respectively.
Along with a definitive number of protons, every element
except hydrogen has one or more neutrons in its nucleus. The
mass number of an atom is the total number of protons and
neutrons in its nucleus. The nucleus of a helium atom con-

tains 2 protons and 2 neutrons; oxygen has 8 protons and 8
neutrons. Therefore, helium has a mass number of 4 and oxy-
gen a mass number of 16. The mass number may be thought
of as the mass of the atom in daltons.
Each element has its own one- or two-letter chemical sym-
bol. For example, H stands for hydrogen, He for helium, and
O for oxygen. Some symbols come from other languages: Fe
(from the Latin, ferrum) stands for iron, Na (Latin, natrium)
for sodium, and W (German, Wolfram) for tungsten.
In text, immediately preceding the symbol for an element,
the atomic number is written at the lower left and the mass
number at the upper left. Thus, hydrogen, carbon, and oxy-
gen are written as
1
1
H,
12
6
C, and
16
8
O, respectively.
Isotopes differ in number of neutrons
Elements can have more than one atomic form. Isotopes of the
same element all have the same, definitive, number of protons,
but differ in the number of neutrons in the atomic nucleus.
In nature, many elements exist as several isotopes. The iso-
topes of hydrogen shown in Figure 2.4 have special names,
but the isotopes of most elements do not have distinct names.
For example, the natural isotopes of carbon are

12
C,
13
C, and
14
C (spoken of as carbon-12, carbon-13, and carbon-14). Most
carbon atoms are
12
C, about 1.1 percent are
13
C, and a tiny
fraction are
14
C. An element’s atomic mass, or atomic
weight,* is the average of the mass numbers of a representa-
tive sample of atoms of the element, with all isotopes in their
normally occurring proportions. The atomic weight of car-
bon is thus calculated to be 12.011.
Some isotopes, called radioisotopes, are unstable and spon-
taneously give off energy as α (alpha), β (beta), or γ (gamma)
radiation from the atomic nucleus. Such radioactive decay
transforms the original atom into another atom, usually of
another element. For example, carbon-14 loses a β-particle
(actually an electron) to form
14
N. Biologists and physicians
can incorporate radioisotopes into molecules and use the
emitted radiation as a tag to locate those molecules or to
identify changes that the molecules undergo inside the body
(Figure 2.5). Three radioisotopes commonly used in this way

are
3
H (tritium),
14
C (carbon-14), and
32
P (phosphorus-32). In
addition to these applications, radioisotopes can be used to
date fossils (see Chapter 22).
Although radioisotopes are useful for experiments and in
medicine, even low doses of their radiation have the poten-
tial to damage molecules and cells. The devastating effects of
radiation from nuclear weapons are well known, as are con-
cerns about possible damage to organisms from isotopes
used in nuclear power plants. In medicine, γ-radiation from
60
Co (cobalt-60) is used to damage or kill cancer cells.
In discussing isotopes and radioactivity, we have focused
on the nucleus of the atom, but the nucleus is not directly in-
volved in the ability of atoms to combine with other atoms.
That ability is determined by the number and distribution of
electrons. In the following sections, we describe some of the
properties and chemical behavior of electrons.
Electron behavior determines chemical bonding
When considering atoms, biologists are concerned primarily
with electrons because the behavior of electrons explains how
chemical changes occur in living cells. These changes, called
chemical reactions or just reactions, are changes in the atomic
*The concepts of “weight” and “mass” are not identical. Weight is the
measure of the Earth’s gravitational attraction for mass; on another

planet, the same quantity of mass would have a different weight. On
Earth, however, the term “weight” is often used as a measure of mass,
and in biology one encounters the terms “weight” and “atomic weight”
more frequently than “mass” and “atomic mass.” Therefore, we will use
“weight” for the remainder of this book.
Hydrogen Deuterium Tritium
1 proton
1 neutron
1 proton
0 neutrons
1 proton
2 neutrons
1
H
2
H
3
H
–
+
–
+
–
+
11 1
2.4 Isotopes Have Different Numbers of Neutrons The isotopes
of hydrogen all have one proton in the nucleus, defining them as that
element.Their differing mass numbers are due to different numbers
of neutrons.
composition of substances. The characteristic number of elec-

trons in each atom of an element determines how its atoms
will react with other atoms. All chemical reactions involve
changes in the relationships of electrons with one another.
The location of a given electron in an atom at any given
time is impossible to determine. We can only describe a vol-
ume of space within the atom where the electron is likely to
be. The region of space where the electron is found at least 90
percent of the time is the electron’s orbital (Figure 2.6). In an
atom, a given orbital can be occupied by at most two elec-
trons. Thus any atom larger than helium (atomic number 2)
must have electrons in two or more orbitals. As Figure 2.6
shows, the different orbitals have characteristic
forms and orientations in space. The orbitals, in
turn, constitute a series of electron shells, or energy
levels, around the nucleus (Figure 2.7).

The innermost electron shell consists of only
one orbital, called an s orbital. Hydrogen (
1
H)
has one electron in its first shell; helium (
2
He)
has two. All other elements have two first-shell
electrons, as well as electrons in other shells.

The second shell is made up of four orbitals
(an s orbital and three p orbitals) and hence can hold up
to eight electrons.
The s orbitals fill with electrons first, and their electrons have

the lowest energy. Subsequent shells have different numbers
of orbitals, but the outermost shells usually hold only eight
electrons. In any atom, the outermost electron shell deter-
mines how the atom combines with other atoms—that is,
how the atom behaves chemically. When an outermost shell
consisting of four orbitals contains eight electrons, there are
no unpaired electrons (see Figure 2.7). Such an atom is stable
and will not react with other atoms. Examples of chemically
stable elements are helium, neon, and argon.
Reactive atoms seek to attain the stable condition of hav-
ing no unpaired electrons in their outermost shells. They at-
tain this stability by sharing electrons with other atoms, or
by gaining or losing one or more electrons. In either case, the
atoms are bonded together. Such bonds create stable associ-
ations of atoms called molecules.
Amolecule is two or more atoms linked by chemical bonds.
The tendency of atoms in stable molecules to have eight elec-
trons in their outermost shells is known as the octet rule. Many
atoms in biologically important molecules—for example, car-
bon (C) and nitrogen (N)—follow the octet rule. However,
some biologically important atoms are exceptions to the rule.
Hydrogen (H) is the most obvious exception, attaining stabil-
ity when only two electrons occupy its single shell.
LIFE AND CHEMISTRY: SMALL MOLECULES 19
Normal thyroid gland Diseased thyroid gland
2.5 A Radioisotope Used in Medicine The thyroid gland takes up
iodine and uses it to make thyroid hormone. A patient suspected of
having thyroid disease can be injected with radioactive iodine,which
allows the thyroid gland to be visualized by a scanning device.
y

y
z
x
1s Orbital
y
z
x
p
y
Orbitalp
x
Orbital
x
p
z
Orbital
z
All p orbitals full
The two electrons closest
to the nucleus move in a
spherical
s
orbital.
Two electrons occupy the 2s
orbital, one of four orbitals in
the second shell of electrons.
y
2s Orbital
z
x

Two electrons form
a dumbell-shaped
x-axis (p
x
) orbital…
Six electrons fill all
three p orbitals.
…two more fill
the p
y
orbital…
…and two fill
the p
z
orbital.
2.6 Electron Orbitals Each orbital
holds a maximum of two electrons.The s
orbitals have a lower energy level and fill
with electrons before the p orbitals do.
20 CHAPTER TWO
Chemical Bonds:
Linking Atoms Together
A chemical bond is an attractive force that links two atoms
together to form a molecule. There are several kinds of chem-
ical bonds (Table 2.1). In this section, we will first discuss co-
Hydrogen (H) Helium (He)
Neon (Ne)
Sodium (Na) Argon (Ar)
Third shell
Second shell

First shell
When all the orbitals in the outermost shell
are filled, the element is stable.
Elements whose outer shells contain unfilled orbitals
(unpaired electrons) are chemically reactive.
Electrons occupying the same
orbital are shown as pairs.
Oxygen has six electrons in its outer
shell and requires two electrons to
achieve stability.
1+
11+
Lithium (Li)
3+
2+
10+
18+
Chlorine (Cl)
17+
Sulfur (S)
16+
Phosphorus (P)
15+
Fluorine (F)
9+
Oxygen (O)
8+
Nitrogen (N)
7+
Carbon (C)

6+
–
–– ––
–
–
––
––
––
– –
–
––
––
–
–
–
–
––
––
––
–
–
–
––
––
––
––
–
–
–
–

––
––
––
–
–
–
–
–
–
–
––
––
––
––
––
–
–
–
–
–
–
––
––
––
––
–
–
–
–
–

–
–
––
––
––
––
––
–
–
–
–
–
–
––
––
––
––
––
–
–
–
–
–
–
–
–
Nucleus
2.7 Electron Shells Determine the Reactivity of Atoms Each
orbital holds a maximum of two electrons,and each shell can hold a
specific maximum number of electrons.Each shell must be filled before

electrons move into the next shell.The energy level of electrons is
higher in shells farther from the nucleus. An atom with unpaired elec-
trons in its outermost shell may react (bond) with other atoms.
Chemical Bonds and Interactions
NAME BASIS OF INTERACTION STRUCTURE BOND ENERGY
a
(KCAL/MOL)
Covalent bond Sharing of electron pairs 50–110
Hydrogen bond Sharing of H atom 3–7
Ionic bond Attraction of opposite charges 3–7
Hydrophobic interaction Interaction of nonpolar substances
1–2
in the presence of polar substances
van der Waals interaction Interaction of electrons of nonpolar
1
substances
a
Bond energy is the amount of energy needed to separate two bonded or interacting atoms under physiological conditions.
2.1
N
C
H
O
H
H
O
C
δ
+
δ

–
N
H
H
N
O
C
H
O
H
H
H
H
C
C
H
H
H
H
C
C
H
H
+
–
C
H
H
H
H

H
H
valent bonds, the strong bonds that result from the sharing
of electrons. Then we will examine other kinds of interac-
tions, including hydrogen bonds, that are weaker than cova-
lent bonds but enormously important to biology. Finally, we
will consider ionic bonding, which is a consequence of the
loss or gain of electrons by atoms.
Covalent bonds consist
of shared pairs of electrons
When two atoms attain stable electron
numbers in their outermost shells by shar-
ing one or more pairs of electrons, a cova-
lent bond forms. Consider two hydrogen
atoms in close proximity, each with a sin-
gle unpaired electron in its outer shell.
Each positively charged nucleus attracts
the other atom’s unpaired electron, but
this attraction is balanced by each elec-
tron’s attraction to its own nucleus. Thus the two unpaired
electrons become shared by both atoms, filling the outer
shells of both of them (Figure 2.8). The two atoms are thus
linked by a covalent bond, and a hydrogen gas molecule (H
2
)
is formed.
A molecule made up of more than one type of atom is
called a compound. A molecular formula uses chemical sym-
bols to identify the different atoms in a compound and sub-
script numbers to show how many of each type of atoms are

present. Thus, the formula for sucrose—table sugar—is
C
12
H
22
O
11
. Each compound has a molecular weight (molec-
ular mass) that is the sum of the atomic weights of all atoms
in the molecule. Looking at the periodic table in Figure 2.3,
you can calculate the molecular weight of table sugar to be
342. Molecular weights are usually related to a molecule’s
size (Figure 2.9).
A carbon atom has a total of six electrons; two electrons
fill its inner shell and four are in its outer shell. Because its
outer shell can hold up to eight electrons, carbon can share
electrons with up to four other atoms—it can form four co-
valent bonds. When an atom of carbon reacts with four hy-
drogen atoms, a molecule called methane (CH
4
)
forms (Figure 2.10a). Thanks to electron sharing, the
outer shell of methane’s carbon atom is filled with
eight electrons, and the outer shell of each hydrogen
atom is also filled. Four covalent bonds—each con-
sisting of a shared pair of electrons—hold methane together.
Table 2.2 shows the covalent bonding capacities of some bi-
ologically significant elements.
ORIENTATION OF COVALENT BONDS
. Covalent bonds are very

strong. The thermal energy that biological molecules ordi-
narily have at body temperature is less than 1 percent of
that needed to break covalent bonds. So biological mole-
cules, most of which are put together with covalent bonds,
are quite stable. This means that their three-dimensional
structures and the spaces they occupy are also stable. A
second property of covalent bonds is that, for a given pair
LIFE AND CHEMISTRY: SMALL MOLECULES 21
Hydrogen molecule (H
2
)
Hydrogen atoms (2H)
…but the nucleus still attracts
its own electron.
If the atoms move closer they
share the electron pair, linking
them in a covalent bond and
forming a hydrogen molecule.
Each electron is attracted to the
other atom‘s nucleus…
H
H
H
H
H
H
Covalent
bond
2.8 Electrons Are Shared in Covalent Bonds Two hydrogen
atoms combine to form a hydrogen molecule.Each electron is

attracted to both protons.A covalent bond forms when the electron
orbitals of the two atoms overlap.
Molecular
weights
Water
18
Glucose
180
Alanine
89
Hydrogen (H)
1
Nitrogen (N)
14
Oxygen (O)
16
Carbon (C)
12
Water is the solvent in
which many biological
reactions take place.
Alanine is one of the
building blocks of
proteins.
Glucose, a sugar, is an
important food substance
in most cells.
2.9 Weights and Sizes of Atoms and Molecules The color con-
ventions used here are standard for the atoms. (Yellow is used for
sulfur and phosphorus atoms,which are not depicted.)

22 CHAPTER TWO
of atoms, they are the same in length, angle, and direction,
regardless of the larger molecule of which the particular
bond is a part. The four filled orbitals around the carbon
nucleus of methane, for example, distribute themselves in
space so that the bonded hydrogens are directed to the cor-
ners of a regular tetrahedron with carbon in the center
(Figure 2.10c). The three-dimensional structure of carbon
and hydrogen is the same in a large, complicated protein
as it is in the simple methane molecule. This property of
covalent bonds makes the prediction of biological struc-
ture possible.
Although the orientations of orbitals and the shapes of
molecules differ depending on the types of atoms involved
and how they are linked together, it is essential to remember
that all molecules occupy space and have three-dimensional
shapes. The shapes of molecules contribute to their biologi-
cal functions, as we will see in Chapter 3.
MULTIPLE COVALENT BONDS
. A covalent bond is represented
by a line between the chemical symbols for the linked atoms:

A single bond involves the sharing of a single pair of elec-
trons (for example, H — H, C — H).

A double bond involves the sharing of four electrons
(two pairs) (C
⎯
⎯
C).

Triple bonds (six shared electrons) are rare, but there is one
in nitrogen gas (N
⎯
⎯
⎯
N), the chief component of the air we
breathe.
UNEQUAL SHARING OF ELECTRONS. If two atoms of the same
element are covalently bonded, there is an equal sharing of
the pair(s) of electrons in the outer shell. However, when
the two atoms are of different elements, the sharing is not
necessarily equal. One nucleus may exert a greater attrac-
tive force on the electron pair than the other nucleus, so that
the pair tends to be closer to that atom.
The attractive force that an atom exerts on electrons is its
electronegativity. It depends on how many positive charges
a nucleus has (nuclei with more protons are more positive
and thus more attractive to electrons) and how far away the
electrons are from the nucleus (closer means more elec-
tronegativity). The closer two atoms are in electronegativity,
the more equal their sharing of electrons will be.
Table 2.3 shows the electronegativities of some elements
important in biological systems. Looking at the table, it is ob-
vious that two oxygen atoms, both with electronegativity of
3.5, will share electrons equally, producing what is called a
nonpolar covalent bond. So will two hydrogen atoms (both 2.1).
Methane, CH
4
1 C, 4 H
C

H
C
(a)
(b)
(c)
C
H
H
H
or
H
C
H
H
H
H
Carbon can complete its outer shell
by sharing the electrons of four
hydrogen atoms, forming methane.
Each line or pair of dots represents
a shared pair of electrons.
This space-filling model shows the shape
methane presents to its environment.
Hydrogens form corners of a
regular tetrahedron.
H
H
H
H
C

H
H
H
H
C
H
H
H
H
H
H
H
Structural formulas
Ball-and-stick model Space-filling model
Bohr models
2.10 Covalent Bonding with Carbon Different
representations of covalent bond formation in
methane,whose molecular formula is CH
4
.(a) Dia-
gram illustrating the filling and stabilizing of the
outer electron shells in carbon and hydrogen atoms.
(b) Two common structural formulas used to repre-
sent bonds. (c) Two ways of representing the spatial
orientation of bonds.
Covalent Bonding Capabilities of Some
Biologically Important Elements
USUAL NUMBER OF
ELEMENT COVALENT BONDS
Hydrogen (H) 1

Oxygen (O) 2
Sulfur (S) 2
Nitrogen (N) 3
Carbon (C) 4
Phosphorus (P) 5
2.2
But when hydrogen bonds with oxygen to form water, the
electrons involved are unequally shared: they tend to be
nearer to the oxygen nucleus because it is the more elec-
tronegative of the two. The result is called a polar covalent
bond (Figure 2.11).
Because of this unequal sharing of electrons, the oxygen
end of the hydrogen–oxygen bond has a slightly negative
charge (symbolized δ
–
and spoken as “delta negative,” mean-
ing a partial unit of charge), and the hydrogen end is slightly
positive (δ
+
). The bond is polar because these opposite
charges are separated at the two ends, or poles, of the bond.
The partial charges that result from polar covalent bonds pro-
duce polar molecules or polar regions of large molecules. Po-
lar bonds greatly influence the interactions between mole-
cules that contain them.
Hydrogen bonds may form within or between atoms
with polar covalent bonds
In liquid water, the negatively charged oxygen (δ
–
) atom of

one water molecule is attracted to the positively charged hy-
drogen (δ
+
) atoms of another water molecule. (Remember,
negative charges attract positive charges.) The bond result-
ing from this attraction is called a hydrogen bond.
Hydrogen bonds are not restricted to water molecules.
They may form between an electronegative atom and a hy-
drogen atom covalently bonded to a different electronegative
atom (Figure 2.12). A hydrogen bond is a weak bond; it has
about one-tenth (10%) the strength of a covalent bond be-
tween a hydrogen atom and an oxygen atom (see Table 2.1).
However, where many hydrogen bonds form, they have con-
siderable strength and greatly influence the structure and
properties of substances. Later in this chapter we’ll see how
hydrogen bonding in water contributes to many of the prop-
erties that make water significant for living systems. Hydro-
gen bonds also play important roles in determining and
maintaining the three-dimensional shapes of giant molecules
such as DNA and proteins (see Chapter 3).
Ionic bonds form by electrical attraction
When one interacting atom is much more electronegative
than the other, a complete transfer of one or more electrons
may take place. Consider sodium (electronegativity 0.9) and
chlorine (3.1). A sodium atom has only one electron in its out-
ermost shell; this condition is unstable. A chlorine atom has
seven electrons in its outer shell—another unstable condition.
Since the electronegativities of these elements are so differ-
ent, any electrons involved in bonding will tend to be much
nearer to the chlorine nucleus—so near, in fact, that there is

LIFE AND CHEMISTRY: SMALL MOLECULES 23
Some Electronegativities
ELEMENT ELECTRONEGATIVITY
Oxygen (O) 3.5
Chlorine (Cl) 3.1
Nitrogen (N) 3.0
Carbon (C) 2.5
Phosphorus (P) 2.1
Hydrogen (H) 2.1
Sodium (Na) 0.9
Potassium (K) 0.8
2.3
O
H
H
H
O
δ
+
δ
–
δ
+
δ
–
δ
+
δ
+
(a)(b)

H
Water’s bonding electrons
are shared unequally;
electron density is greatest
around the oxygen atom.
Unshared pairs of
electrons are not
part of water's
covalent bond.
Water has polar
covalent bonds.
2.11 The Polar Covalent Bond in the Water Molecule (a) A cova-
lent bond between atoms with different electronegativities is a polar
covalent bond, and has partial (δ) charges at the ends. (b) In water,
the electrons are displaced toward the oxygen atom and away from
the hydrogen atoms.
H
O
H
H
O
H
δ
–
H
N
δ
+
δ
–

O
C
δ
+
δ
–
δ
–
δ
+
δ
+
δ
+
δ
+
Polar
covalent
bonds
Hydrogen
bonds
Two water molecules Two parts of one large molecule
(or two large molecules)
The hydrogen bond
is a weak attraction
shared between two
electronegative
atoms.
2.12 Hydrogen Bonds Can Form between or within Molecules
Hydrogen bonds can form between two molecules or,if a molecule

is large,between two different parts of the same molecule.Covalent
and polar covalent bonds, on the other hand,are always found within
molecules.
24 CHAPTER TWO
a complete transfer of the electron from one element to the
other (Figure 2.13). This reaction between sodium and chlo-
rine makes the resulting atoms more stable. The result is two
ions. Ions are electrically charged particles that form when
atoms gain or lose one or more electrons.

The sodium ion (Na
+
) has a +1 unit charge because it has
one less electron than it has protons. The outermost elec-
tron shell of the sodium ion is full, with eight electrons, so
the ion is stable. Positively charged ions are called cations.

The chloride ion (Cl
–
) has a –1 unit charge because it has
one more electron than it has protons. This additional
electron gives Cl
–
a stable outermost shell with eight elec-
trons. Negatively charged ions are called anions.
Some elements form ions with multiple charges by losing or
gaining more than one electron. Examples are Ca
2+
(calcium
ion, created from a calcium atom that has lost two electrons)

and Mg
2+
(magnesium ion). Two biologically important ele-
ments each yield more than one stable ion: Iron yields Fe
2+
(ferrous ion) and Fe
3+
(ferric ion), and copper yields Cu
+
(cuprous ion) and Cu
2+
(cupric ion). Groups of covalently
bonded atoms that carry an electric charge are called complex
ions; examples include NH
4
+
(ammonium ion), SO
4
2–
(sulfate
ion), and PO
4
3–
(phosphate ion).
The charge from an ion radiates from it in all directions.
Once formed, ions are usually stable, and no more electrons
are lost or gained. Ions can form stable bonds, resulting in
stable solid compounds such as sodium chloride (NaCl) and
potassium phosphate (K
3

PO
4
).
Ionic bonds are bonds formed by electrical attraction be-
tween ions bearing opposite charges. In sodium chloride—
familiar to us as table salt—cations and anions are held to-
gether by ionic bonds. In solids, the ionic bonds are strong
because the ions are close together. However, when ions are
dispersed in water, the distance between them can be large;
the strength of their attraction is thus greatly reduced. Under
the conditions that exist in the cell, an ionic attraction is less
than one-tenth as strong as a covalent bond that shares elec-
trons equally (see Table 2.1).
Not surprisingly, ions with one or more units of charge
can interact with polar molecules as well as with other ions.
Such interaction results when table salt, or any other ionic
solid, dissolves in water: “shells” of water molecules sur-
round the individual ions, separating them (Figure 2.14). The
hydrogen bond that we described earlier is a type of ionic
bond because it is formed by electrical attraction. However,
it is weaker than most ionic bonds because it is formed by
partial charges (δ
+
and δ
–
) rather than by whole-unit charges
(+1 unit, –1 unit).
Polar and nonpolar substances interact best
among themselves
“Like attracts like” is an old saying, and nowhere is it more

true than in polar and nonpolar molecules, which tend to in-
teract with their own kind. Just as water molecules interact
with one another through polarity-induced hydrogen bonds,
any molecule that is itself polar will interact with other polar
molecules by weak (δ
+
to δ
–
) attractions in hydrogen bonds. If
a polar molecule interacts with water in this way, it is called
hydrophilic (“water-loving”).
What about nonpolar molecules? For example, carbon
(electronegativity 2.5) forms nonpolar bonds with hydro-
gen (electronegativity 2.1). The resulting hydrocarbon mole-
cule—that is, a molecule containing only hydrogen and car-
bon atoms—is nonpolar, and in water it tends to aggregate
with other nonpolar molecules rather than with polar wa-
ter. Such molecules are known as hydrophobic (“water-
hating”), and the interactions between them are called
hydrophobic interactions. It is important to realize that hy-
drophobic substances do not really “hate” water; they can
form weak interactions with it (recall that the electronega-
tivities of carbon and hydrogen are not exactly the same).
But these interactions are far weaker than the hydrogen
bonds between the water molecules, and so the nonpolar
substances keep to themselves.
– – –– –
–
–
–

–
–
–
–
–
–
–
–
Sodium atom (Na)
(11 protons, 11 electrons)
Chlorine atom (Cl)
(17 protons, 17 electrons)
–
– – –– –
–
–
–
– –
–
The atoms are now electrically
charged ions. Both have full electron
shells and are thus stable.
Chlorine “steals” an
electron from sodium.
– – –– –
–
–
–
–
–

–
–
–
–
–
–
Sodium ion (Na
+
)
(11 protons, 10 electrons)
Chloride ion (Cl
–
)
(17 protons, 18 electrons)
–
–
+
–
–
– –
–
–
–
– –
–
–
Ionic
bond
2.13 Formation of Sodium and Chloride Ions When a sodium
atom reacts with a chlorine atom, the more electronegative chlorine

acquires a more stable,filled outer shell by obtaining an electron
from the sodium. In so doing, the chlorine atom becomes a negative-
ly charged chloride ion (Cl
–
).The sodium atom, upon losing the elec-
tron, becomes a positively charged sodium ion (Na
+
).
These weak interactions between nonpolar sub-
stances are enhanced by van der Waals forces, which
result when two atoms of nonpolar molecules are in close
proximity. These brief interactions are a result of random
variations in the electron distribution in one molecule,
which create an opposite charge distribution in the adja-
cent molecule. Although a single van der Waals interac-
tion is brief and weak at any given site, the summation of
many such interactions over the entire span of a large non-
polar molecule can produce substantial attraction. van der
Waals forces are important in maintaining the structures
of many biologically important substances.
Chemical Reactions: Atoms Change Partners
A chemical reaction occurs when atoms combine or
change their bonding partners. Consider the combustion
reaction that takes place in the flame of a propane stove.
When propane (C
3
H
8
) reacts with oxygen gas (O
2

), the car-
bon atoms become bonded to oxygen atoms instead of to
hydrogen atoms, and the hydrogen atoms become bonded
to oxygen instead of carbon (Figure 2.15). As the covalently
bonded atoms change partners, the composition of the mat-
ter changes, and propane and oxygen gas become carbon
dioxide and water. This chemical reaction can be represented
by the equation
C
3
H
8
+ 5 O
2
→ 3 CO
2
+ 4 H
2
O + energy
2.14 Water Molecules Surround Ions When an ionic solid dissolves
in water,polar water molecules cluster around cations or anions,
blocking their reassociation into a solid and forming a solution.
Propane
Reactants
Products
Oxygen gas Carbon
dioxide
Water
+
+

+
+
+
+
+
+
Heat and light
+
Energy
C
3
H
8
5 O
2
3 CO
2
4 H
2
O
2.15 Bonding Partners and Energy May Change in a
Chemical Reaction One molecule of propane reacts
with five molecules of oxygen gas to give three mole-
cules of carbon dioxide and four molecules of water.This
reaction releases energy in the form of heat and light.
–
+
+
–
+

+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+

+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+

+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+

+
–
+
+
–
+
+
–
+
+
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–

–
–
–
–
–
–
–
–
–
–
–
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
++
+
+
+

+
+
+
+
+
+
+
+
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–
–

–
–
–
–
–
–
–
–
–
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

+
+
+
+
+
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+

+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
–
–
–
–
–
–
–
–
–
–
–
–
–

–
–
–
–
–
+
+
+
+
+
+
+
+
+
+
+
+
+
+
–
+
+
–
+
+
–
+
+
–
+

+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+

+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–

Undissolved
sodium
chloride
Undissolved
sodium
chloride
Water molecules
Chloride ion
(Cl
–
)
Sodium ion
(Na
+
)
–
+
+
+
–
+
+
–
+
+
–
+
+
–
–

+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
–
–
+
+
–
+
+
–
+
+
–
+

+
–
+
+
–
+
+
–
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
+
–
+
+

–
+
+
–
+
+
–
+
+
–
+
+
–
+
+
+
When NaCl is dissolved in
water, the chloride anion (–)
attracts the + pole of water…
… and the sodium cation (+)
attracts the – pole of water.
Ionic bonds between
Na
+
and Cl
–
hold ions
together in a solid crystal.
25